I first want to point out that the transitions that we dealt with in Polymer 2 and Polymer 3 we mostly out of our control. The Web Components v1 spec we just different in some important ways, and we tried our best to ease that transition in Polymer 2 with hybrid mode. Then HTML Imports was clearly not going to be adopted while JS modules were implemented in every browser, and Bower was deprecated and didn't have many important packages available on it. We tried to mitigate those transitions by not changing the Polymer 3 API at all and building Modulizer.
But there's really not much we can do about libraries that haven't made the transition. There really isn't a way to import HTML Imports into JS, which is one of the reasons it didn't get adoption. The difficulty of using Polymer 2 components in Polymer 3 is the same difficulty that the entire rest of the web development ecosystem has had with Polymer until Polymer 3.
The best thing going is that if the components you use are open source they can be forked and converted, and again, the Polymer API itself didn't change.
The good news is that the Web Components v1 specs are stable and implemented in 3 major engines and in-development in the 4th. So we won't have a Polymer 1 -> Polymer 2 like transition again. And JS modules are implemented in all engines, and the whole ecosystem has coalesced around npm, so we won't have a Polymer 2 -> Polymer 3 like transition again.
What we will have is much smoother, incremental transitions like Polymer -> LitElement, where we can easily mix and match components from different vendors or built with different helper libraries. The largest barrier there is needing to manually listen for Polymer's {property}-changed events to implement 2-way data-binding if you use that, and there are helpers for that popping up. There's no application-wide blocker like incompatible specs or package managers.
So I apologize for the pains, and we really have tried to minimize them. The only way this could have been avoided though, would be if the Web Component v0 specs, including HTML Imports, were implemented by all browsers, and the ecosystem coalesced around Bower. That just didn't happen though.
Cheers,
Justin